A Light in the Darkness
by packleader96
Summary: After surviving an attempt on their lives, Twilight and Shining Armor find themselves being targeted by a pony determined to have revenge, and as they delve deeper into the mystery, they will discover dark things about their family's past, and how it affects them. Rated T for Language, Violence, and Some Sexuality. (post Equestria Girls)
1. Prologue

**A/N: hey guys, I've had this idea floating around in my head for some time now, and I finally decided to write it and see how it turns out, I'll let you readers decide if you like it or not, enjoy.**

**A Light in the Darkness: prologue**

(Unknown location)

A young male earth pony walked down the hall of an abandoned building, he looked at the two guards escorting him, as they continued walking down the lite hallway, they turned to the door on their left which had two other guards standing in front, the earth pony watched as the other guards opened the door and they stepped inside, where there was a large map spread across the table, with one pony looking over, his back facing them, one of the guards cleared his throat as the pony turned around, revealing to be a unicorn, but that was not the most interesting feature on his face, he had a long jagged scar running down his left cheek, through his eye, which was clouded.

As they walked in, the unicorn smiled, "ah, I'm glad your finally here, I hope my guards weren't too rough with you" he said as he walked around the table, the earth pony took a step forward, "well, when I got your letter, saying you had a job to be done, with that amount of caps, I couldn't refuse" he said, the unicorn smiled, "excellent, I sent the letter to you and your friends because, your team has a particular skill that I need, a skill in assassination" he said with an amused look.

The earth pony cleared his throat, "yes we do, what's the job, who's the target?" he asked, the unicorn placed a two folders on the table and slid them forward, "not target, targets, I want to test your abilities" he said, the earth pony flipped each folder open and looked at the pictures of the targets, as soon as he did his eyes widened in shock, and he placed the pictures down, "you must be crazy, nopony can pull off a job like this, this is too big" he said, the unicorn just smiled, "really, if you succeed, I'll pay you double, all the information is right here, all the planning has been done for you, all you have to do is go there, kill the targets and return to me, simple as that" he said with a sinister smile.

The earth pony looked over all the information again, checking everything, and making sure it was all right, the entire thing had been planned out, just like he said, he looked up at the unicorn and swallowed, and then did his best to smile, "alright, I'll get my best guys together, but you had better have our money waiting" he said as he was escorted out of the room, the unicorn looked down at the folders and pulled them back in front of him, as another pony, a Pegasus, walked into the room.

"boss, are you sure it's really necessary paying them that much, you know they'll fail, in fact you've planned for them to fail, so why go through all this, just to get to them, when you could take care of them yourself?" he asked, the unicorn sighed and looked up at him, his scar making the Pegasus uneasy.

"your my most trusted lieutenant, but there are something's you shouldn't know, yes I know they'll fail, that's why I have offered so much money, to convince them to do the job, but they'll fail, this whole thing is just a setup" he said opening the folders and looking at the two pictures, the Pegasus took a step forward, "a set up for what sir?" he asked, the unicorn smiled, "the game of course, this is merely the setup, before every game, the pieces must be set into place, and this is my first move" he said standing up and looking at the pictures.

"I've waited over twenty years for this, planning, planning my revenge, and now…it's time I take it" he said placing the pictures of the map, and walking past the Pegasus, who just watched him go for a minute, and then turned to the map and walked over, he slowly picked up the pictures, and looked at them, his eyes widened as too who the targets were, in his hooves, was none other than a picture of the newly crowned Princess Twilight Sparkle, and her older brother, Prince Shining Armor, the Pegasus put the pictures down and calmly walked out of the room.

**A/N: well that's it for now my friends, like I said this will be a bit of test run for this story, and if you all like it, then I shall continue, if not…we'll get to that later, hope you enjoyed, peace.**


	2. Chapter 1

**A/N: well, I got a chance to write in between my homework schedule, so let's get it done, hope you enjoy this chapter.**

**A Light in the Darkness: chapter 1: a good day gone very bad**

Princess Twilight and all her friends eagerly watched as their train pulled into the Crystal Empire's train station, as it jerked to a stop they all stepped out and walked on to the platform, the shining castle towering above the others, gleaming in the sunlight.

"wow, this places looks better and better, every time we come here" Rarity commented as they started down the road, they all chuckled, "yeah, Cadence and Shining Armor have really done a great job at restoring this place" Twilight said as they headed for the castle entrance.

As they walked into the castle, they saw all sorts of guards standing by the entrance, when they saw them coming, they used their magic to open the doors, and as Twilight and her friends walked in, they saw a group of guards waiting for them, with a particularly familiar Pegasus guard standing there, Twilight instantly recognized him as the newest member of her guard, Flash Sentry.

As they walked up, he smiled and gave a bow, Twilight simply blushed, "welcome your highness, Princess Cadence and Prince Shining Armor are waiting for you in the throne room, please follow me" he said as he turned and lead them down the hall, as they walked, Rarity leaned over and whispered to Twilight, "Twilight darling, I still don't understand it, we all know you like him, you should ask him out, or he should ask you" she said quietly.

Twilight's blushed deepened as she turned to her, "if you're thinking that I have a crush on him, your wrong, I just think he's a nice guy, he's very committed to his duty as a guard" she said as they were being lead to the throne room, while they walked she could hear Rainbow Dash whisper to Applejack, "that's code for 'I think he's the cutest guy ever'" she said and they all laughed, Twilight looked back at her with an evil glare.

After another minute or two, they came to the large door of the throne room, the two unicorn guards open it with their magic, and they all walk in, as they cross into the room, they look up to see Cadence sitting on her throne, but no sign of Shining Armor, when they got closer they saw that she was talking with one of their advisor's, flash took a step closer and cleared his throat, catching her attention.

"I apologize if I was interrupting, but Princess Twilight and her friends are here" he said with a bow, Cadence looked at them and smiled widely, as she walked down to them, Twilight happily walked toward her and they hugged, "oh Twilight it's so good to see you, I hope the train ride wasn't boring or anything, we really need to get together more often" she said with a kind smile, Twilight simply smiled back, "we sure do, hey, where's Shining?" she asked looking around, Cadence smiled, "oh I'm sure he's around somewhere, we'll see him at dinner, speaking of which, it's getting around that time, and I'm sure you all must be hungry, were trying a traditional Crystal Empire dish, it's amazing what you find from a kingdom that's been lost for centuries, come, we'll head to the dining room"

(Crystal Empire castle, dining room)

As they entered the dining room, they saw a large table there, that was already neatly set up, candles lined the table, with plates in all the positions, all placed at the ten available spots around it, as they got to their seats, the door on the other side of the room opened and in walked Shining Armor, a smile on his face as he turned to Twilight, "Twiley, glad to see you made it here okay, sorry I couldn't meet you at the station, but I had some important captain duties to tend to" he said with a smile, as he walked over and hugged her, she hugged back.

"it's no problem, we got here just as fine" she said, Shining smiled and walked over and gave his wife a kiss on the cheek, before taking a seat diagonal from her, only a few minutes passed before the door to the kitchen opened and a large group of ponies came walking out, all carrying trays of food, Twilight and all her friends watched in excitement as the butlers set the food down in front of them "everypony enjoy, the food is made from the finest ingredients here in the empire" the main butler said as they all stood by.

(Later that night…)

As they all sat and ate their dinner, they continued to laugh and tell jokes, Cadence told those stories of all the interesting things they had discovered about the empire in the past few weeks alone, while Shining told them all the hilarious stories of the things Twilight and him did as foals, much to her embarrassment.

After a while Cadence looked at the clock on the wall, and saw that it was already late, she looked out of the window and saw that the sun had already set, she quickly stood up, "well, time sure does fly, it's already night time, I believe we should all be going to bed now, we can talk more tomorrow, Shining and I will give you a tour of all the places we've discovered" she said as she calmly walked out of the room, Shining looked up at the clock and nodded his head before standing up, and following her out of the room.

Twilight and all her friends watched as Flash a group of guards walked up to them, "pardon me, but I've been instructed to take you to your rooms, if you'll follow me please" he said, Twilight and all her friends looked at each other and then stood up and followed him out of the room.

(Later…)

After leaving the dining hall, Flash and the other guards escorted Twilight and her friends to their rooms, Flash calmly opened the door, and Twilight walked in, while another guard set her bag on the bed, and left them, "well, here you are, I hope it's too your liking" he said calmly, Twilight turned to him and smiled, "oh yes it is, tell me something Flash, how long have you been in the guard?" she asked, the question seemed to catch him by surprise slightly, but he sighed, "well, I've been in the guard for about a year now, but I actually just got out of training about 3 months ago" he said with pride, Twilight smiled, "so tell me, what's it like training under by brother?" she asked, a startled look appeared on his face, but she simply chuckled.

"It's okay, you can tell me, I won't get mad or anything" she said and his worry subsided, "well to be honest your highne-" but she cut him off by raising her hoof, "please, just call me Twilight" she said kindly, he felt a wave of relief wash over him, "well with all due respect your high- I mean Twilight, it was kind of scary, your brother can be very…persuasive with his words" he said with a nervous chuckle, and Twilight giggled, "well I'll give you that, he's a very strong-willed stallion" she said, and Flash spoke up, "but don't get me wrong, your brother's a great captain, he's very inspiring and thoughtful, but if he found out that I was talking to you, without addressing you as 'your highness' he'd probably chew my head off" he said, and they both let out a burst of laughter.

After they calmed down, Twilight took a step closer to him, "you know Flash, you're…different from the other guards, and that's why I like you" she said, she smiled at the nervous look on his face, "what do you mean by that?" he asked nervously, "I mean that you're not like them, the other guards, they simply just salute me, or tell me 'yes, your highness' which can get a little annoying, but you're the only one who actually cares to have a normal conversation with me, despite my royal status, you treat me like any other pony" she said with a smile, he smiled back and blushed slightly.

"Well with all due respect, I believe that even a Princess needs friends too, not to say you have any need for more friends, your friends are great, they all seem very loyal and supportive of you" he said with a calm expression, she smiled at him and blushed, "there's no such thing as having to many friends, who knows, maybe we can get together every now and then and have a little chat, how about it, maybe…when we return to Canterlot, we can go get a smoothie together sometime" she said with a kindly smile, Flash felt sweat running down his forehead, was she asking him out?, Shining would surely have his rear end for this, but still, his answer even surprised him.

"I…I think that would be very nice, well I should let you get settled in, have a good night, if you need anything, there will be some guards outside your door, goodnight Princess" he said as he closed the door.

Twilight smiled and walked over to the bed, and as she started putting her things away, she couldn't stop thinking about him, he really was different from the other guards, he treated her like a normal pony, but still gave her the respect of being a Princess, and that's what she liked about him, he was very caring and sensitive, and he wasn't afraid to talk to her, in fear of her brother.

She sighed happily as she crawled into bed, and pulled the sheets up, levitating her crown onto the night stand, and placing her head on to the pillow, and closing her eyes, and let sleep take her, as her mind became filled with happy thoughts.

(Cadence and Shining Armor's room)

As they both got ready for bed, Shining was in the bathroom brushing his teeth, while Cadence pulled out her mane styles, and let her mane fall down, "you know, it's nice having Twilight and her friends around, especially when there's no national threats to deal with" she said, Shining chuckled as he came into the room, "yeah well, but you have to admit it's more exciting that way" he said as he walked up to her.

She smiled at him, "you know something else, I can't help but notice, that one of our guards, Flash Sentry, has taken quite an interest in Twilight" she said, and Shining gave her a suspicious look, "oh, and how do you know this?" he asked, Cadence smiled at him, "when you're the goddess of love, you can't help but notice things, and don't go off the edge with this, it's just something I happened to notice, but I can tell she likes him back, you know just as well as I do, that Twilight is more than old enough to find a Coltfriend, she's getting to that edge where she won't need her big brother protector anymore" she said, Shining sighed, "yeah I know, but I just can't help it, she is my little sister, and she'll always be, no matter how old she gets, but I just can't help but feel cautious for her" he said with a sigh.

Cadence crawled into their large bed, and cuddled up to him, "I know, and it's perfectly natural, but you'll eventually need to trust her with her own decisions" she said and kissed him, he smiled at her, "maybe your right, but I'll still keep an eye on her" he said with a chuckle, his wife rolled her eyes and turned away with an amused smile, "goodnight sweetie" she said, Shining chuckled to himself and closed his eyes.

**A/N: well, that was a nice sentimental chapter, but sadly it will end, as the next chapter things will pick up, hope you enjoyed, and see you next time, peace.**


	3. Chapter 2

**A/N: well since I don't have much homework, I decided to write another chapter for this story, and do the homework later, here it is, hope you enjoy.**

**A Light in the Darkness: chapter 2: the unexpected visitors**

Night had fallen over the Crystal Empire, and almost all ponies were asleep, the castle had nearly gone quiet, save for the guards that roamed the halls, making sure everything was alright, since Twilight's crown had been taken, the security had been doubled, and that Twilight and all the others had guards standing outside of their doors.

The two guards standing outside princess Twilight's room, kept a careful watch, they waited through the night, and watched as one of the guards walked by them on his nightly patrol, "anything out of the ordinary?" he asked walking up to them, they both shook their head, "no, it's been as quiet as a graveyard around here" one of the guards said, the third nodded, "alright then, call if you need assistance" he said as he continued walking.

They watched until he turned the corner, a few seconds past, when they heard a loud thud, and they immediately turned and looked for the source, it had come from the direction of the other guard, "hey, you okay over there?" one of them asked, but the only response they got was silence, they turned to look at each other, one of them nodded and walked down the hall, where he used his horn as a flashlight, he quickly turned the corner, the first guard waited for a minute, and heard nothing.

Then all of a sudden, there was a cry of surprise and another thud, this time he saw something clang to the floor, he took a step towards it, and saw that it was a helmet, his eyes widened in panic, as he began looking in all directions, he brought his hoof up to the earpiece, "hello, HQ come in, we've got a situation, I have two officers down, do you copy" he said, there was static at first, but then a voice answered, _"roger that, are you sure you have confirmation?"_ the voice asked, he was about to answer, when he felt a blow to the back of the head, and then everything went black.

The black cloaked figure stood above the unconscious body of the guard, and smiled as he stepped on the earpiece, he looked in all directions, and turned to the door, he slowly brought his hoof up and turned the know gently, and slowly began to push the door open, letting the light fill the room, he poked his head and saw his target sleeping in her bed, princess twilight.

(Crystal Empire castle, security center)

"Hello, are you there, have you or have you not confirmed two officers down, answer me" the operator demanded, noticing the distress in his voice, Flash walked over to him, "what's the problem?" he asked, the guard turned to him, "one of our guards reported two unconscious guards, I tried to ask him, but the line went dead" he said with a concerned tone, "where was it coming from?" he asked, the pony turned to the screen and pressed a few keys, "it came from…the guards on the fourth floor corridor" he said, Flash felt a wave of concern wash over him, "bring up some images" he said, the operator pressed a few more keys, and then another screen popped up, revealing a black cloaked figure knocking out a guard.

Flash felt his skin crawl, "that's…that's princess Twilight's room" he said in shock, they watched as the figure slowly opened the door, and walked in, closing it behind him, "shit, get some guards up there now, and sound the alarm!" he shouted as he ran out of the room.

(Meanwhile…)

The cloaked pony slowly walked across the room, making sure not to make any noise, the light from the hall, shining right to the bed, the young mare seemed to be sleeping peacefully, a smile on her face, as he approached the bed, he reached under his cloak, and unsheathed a hidden knife, and stepped next to the bed, so he could see her face, he took a deep breath and began to raise the knife up, just as he did, he heard a loud bell noise fill the room, and a flashing red light, he turned to see his target open her eyes.

It was the loud bell ringing noise that woke Twilight up, she opened her eyes to see a looming cloaked figure, standing above her, she looked up to see the knife he was holding, she cried out in shock and fear, the figure yelled out as he brought the knife down, Twilight quickly rolled out of the way, and on to the floor, she quickly stood up, only to see the assassin jump over the bed at her, but she dodged out of the way, and he crashed into the wall, now wide awake.

"Who are you, what do you want?" she asked, but the assassin turned to her with a growl, ad lunged at her again, swinging the knife, Twilight cried out in pain as the edge of the blade cut her cheek slightly, and then get smacked to the ground, she rolled on to her back, and turned to face him who was looming over her, "stop this, the guards will be here any second" she tried to sound brave but failed, the pony chuckled, "oh don't hold your breath, I've taken care of them, sorry but our employer has paid us quite a lot of money, to kill you and your brother" he said, Twilight's eyes widened in shock, "Shining Armor?" she said, but he quickly raised the knife, but before he could slash at her, the door flew open and familiar voice called out, "your highness!" the voice shouted, Twilight turned to see Flash pointing a crossbow at the assassin.

Flash pointed the bow at him and pulled the trigger, the bow hit the knife out of his hand, the assassin cried out and held his hoof, Flash took the opportunity, and charged forward, slamming into the assassin's side, "your highness run!" he shouted as he tried to hold him down, Twilight just kept watching, the assassin got his footing and punched Flash in the stomach, and head-butted him, and finally threw him into the wall.

Flash cried out in pain as the wind was knocked out of him, and he was slammed into the wall, "why you little…" the assassin cried out as he took out another knife and charged at him, Flash looked up in fear, and closed his eyes, but instead of feeling pain, he heard a blast of magic and a cry of pain, he looked up to see that Twilight blasted him with bolt of magic and knocked him out.

He turned to look at her and saw the scared look on her face, he quickly got up and ran to her, he put his hoof around her, "Princess Twilight are you alright?" he asked she looked up at him with concern and nodded, "my brother, Shining Armor, he's in danger, we need to help him" she said, Flash nodded as guards came into the room, "secure him, then meet me at Prince Shining Armor's room, and hurry" he said as they both ran out the door.

(Cadence and Shining Armor's room)

When the alarm went off, Shining armor shot up in bed, as the room filled with a pulsing red light, Cadence sat up as well, "what is that?" she asked, Shining got out of bed, and looked around, "it's the emergency alarm system, it goes off when there's an intruder in the castle, come on, we need to get to the throne room" he said, as Cadence got out of bed, Shining went up to the cabinet, and got out the knife that was part of his armor set, just as he did, the door opened, and he spun around, only to see a royal guard enter.

"Guard, what's going on?" he demanded, the guard walked up to him, "there's an intruder in the castle, I was sent to check on you" he said, Shining put the knife down and walked up to him, "what about my sister and her friends, where are they?" he asked, the guard looked away for a second, "there…headed for the throne room" he said, Shining picked up the knife and Cadence walked over to him, "well let's go, we'll meet them there" he said as they walked toward the door, but stopped when they heard a bow being pulled back on a crossbow.

Shining and Cadence slowly turned to see the guard pointing the crossbow at them, "what is this?" Shining demanded, the guard smiled evilly, "sorry Captain, but I can't let you get out of here alive, you really should choose your guards more carefully" he said as he pulled the trigger, Shining thought quick and jumped to the side, but cringed as the arrow cut his shoulder, enough to make it bleed.

He landed and held his shoulder, the assassin growled and pulled out a knife and lunged at him, swinging his knife, Shining brought up his and blocked it, the assassin swung again and shining dodged to the side, and rammed him, the assassin cried out in pain, and landed with a thud, Shining got up, and ran over to Cadence, "let's get out of here" he said, but before they moved Cadence saw the assassin stand up and charge at him, "Shining behind you!" she cried out as her horn glowed and a blast of magic shot at him and knocked him against the wall, unconscious.

Shining looked back at the assassin and then at his wife, just as she ran up to him and hugged him, he hugged her back, and just as the door flew open, Shining pointed the knife, but to his surprise, his sister and Flash sentry stood in the door, "Twiley…" he said, Twilight ran up to him and hugged them both, "are you two okay, what happened?" she asked, Cadence replied, "were fine, what about you, how did you escape?" she asked, Twilight looked at her, "I'm fine, thanks to Flash, he got there just in time, or…let's not go there, we captured the assassin" she said, as more guards arrived to arrest the assassin.

After making sure everything was checked out, they made their way to the throne room, where they would find out what to do next, and why the assassins attacked them.

All the injured guards, were tended too, Twilight's friends rushed into the room, all asking a flurry of questions, "Twilight, we heard what happened, are you alright?" Applejack asked, Twilight smiled and nodded, "yes, I'm fine, Flash got there just in time to arrest the assassin, with my help of course" she said with a smile, as they all continued talking.

Shining watched with a smile, thankful that his family was safe, he turned to see Flash tending to a wounded guard, and calmly walked over to him, "Private Sentry, status report" he said, Flash turned to look at him and stood up, and saluted him, "sir, no casualties, all the unconscious guards are being taken to the medical wing, let's be thankful nopony was killed in this mess" he said as he relaxed slightly, Shining smiled at him.

"Indeed, let's be thankful of that, what of the assassins?" he asked, Flash looked him in the eyes, "their being taken to the holding cells in the dungeon, we'll get in contact with Canterlot in the morning" he said, Shining smiled and nodded, "well, I heard you saved my sister's life, you have my deepest gratitude, I could tell you were a good soldier, not afraid to risk your life, in protection of royalty" he said, Flash felt himself getting nervous, "yes sir, I couldn't stand by and let something bad happen to her, I did what I knew was right, to be truthful she saved me as well, I just did what was right, nothing more" he said, and Shining laughed.

"indeed, but you mustn't be so modest, you saved her life, and I am grateful to you, and as reward for your great service, I am promoting you to Corporal, congratulations" he said extending his hoof out, Flash felt his heart beat against his chest, he looked at Shining and smiled widely, and shook his hoof, "thank you sir, you don't know what this means to me, I promise you won't regret this" he said as he let go and saluted, and walked away, Shining watched him go with an amused smile.

He quickly turned and made his way out of the room, this was going to be hard to explain with the Princess's.

**A/N: well there you have it for now, that's all I got, keep an eye out, because things are only going to get more interesting, hope you enjoyed.**


End file.
